Related papers: The entropic lock and key of the histone code
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
Magnetic interfaces and the phenomena arising from them drive both the design of modern spintronics and fundamental research. Recently, it was revealed that through designing magnetic frustration in configurationally complex entropy…
A malleable coding scheme considers not only compression efficiency but also the ease of alteration, thus encouraging some form of recycling of an old compressed version in the formation of a new one. Malleability cost is the difficulty of…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
Topological quantum many-body systems, such as Hall insulators, are characterized by a hidden order encoded in the entanglement between their constituents. Entanglement entropy, an experimentally accessible single number that globally…
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers,…
We present for static density functional theory and time-dependent density functional theory calculations an all-electron method which employs high-order hierarchical finite element bases. Our mesh generation scheme, in which structured…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Large-scale DNA deformation is ubiquitous in transcriptional regulation in prokaryotes and eukaryotes alike. Though much is known about how transcription factors and constellations of binding sites dictate where and how gene regulation will…
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long distance regulatory interactions. The mechanistic basis…
Donor-based quantum devices in silicon are attractive platforms for universal quantum computing and analog quantum simulations. The nearly-atomic precision in dopant placement promises great control over the quantum properties of these…
In lymphoma, mutations in genes of histone modifying proteins are frequently observed. Notably, somatic mutations in the activatory histone modification writing protein MLL2 and the repressive modification writer EZH2 are the most frequent.…
It has been suggested that the minimization of the probability for lethal mutations is a major constraint shaping the genetic code, with the finding that the genetic code is highly protective against transition mutations. Here, we show that…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
Nonbenzenoid carbon frameworks expand low-dimensional material design via controlled asymmetry. Here, we show the experimentally realized 4-5-6-8 carbon nanoribbon establishes a topology-driven paradigm for multiproperty engineering, not…
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…
It is demonstrated in the (pseudo)spin S=1 formalism that the structure of antiphase domain boundaries in the phase of charge ordering of a mixed-valence system of the Cu1+, 2+, 3+ "triplet" type in cuprates on a two-dimensional square…
In this article, we consider a 2 factors-model for pricing defaultable bond with discrete default intensity and barrier where the 2 factors are stochastic risk free short rate process and firm value process. We assume that the default event…
We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated…